phase_shapeit: Strelka wrapper for SNV variant calling

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Strelka wrapper for SNV variant calling

Description

This function wraps the STRELKA functions for variant calling

Usage

phase_shapeit(
  bin_bcftools = build_default_tool_binary_list()$bin_bcftools,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  bin_shapeit = build_default_tool_binary_list()$bin_shapeit,
  ref_panel = build_default_reference_list()$HG19$phasing$G1000$new$vcf,
  gmap = build_default_reference_list()$HG19$phasing$G1000$new$gmap,
  vcf = NULL,
  chr = c(1:22, "X"),
  scaffold = NULL,
  output_name = NULL,
  ...
)

Arguments

bin_shapeit	Path to SHAPEIT binary file
vcf	Path to VCF file
haplotype	Path to haplotype information from 1000G
legend	Path to legend information from 1000G
map	Path to map information from 1000G

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.